uMAIA 0.1

Toolbox for the processing and analysis of MALDI-MSI data

uMAIA

Toolbox for the processing and analysis of MALDI-MSI data

Installation

To begin, install the environment by navigating to the /uMAIA directory and running python3 setup.py. The command was tested with Python version 3.7.16.

Gurobi

The molecule matching portion of the pipeline requires Gurobi. You will need to (1) install the Gurobi installer and (2) activate a license that is free for those are affiliated with an academic institution. Concerning (1), download the archive with

wget https://packages.gurobi.com/9.1/gurobi9.1.2_linux64.tar.gz to the directory you want to install it in.

Unpack the archive with

tar -xzvf gurobi9.1.2_linux64.tar.gz

Activate the license with

gurobi912/linux64/bin/grbgetkey <licensekey>

GPU usage restrictions

If you intend on applying uMAIA's normalisation algorithm on a GPU, please note that JAX will automatically use between 75 and 90 % of available GPU memory. To indicate that you would only like to allocate memory that is needed, you may export an environment variable after activating the environment with export XLA_PYTHON_CLIENT_PREALLOCATE=false